This issue is being reported by other users in various forums including the HTC Support forums...
The standard HTC Clock/Weather widget on the home screen is supposed to call up the Clock app if you press on the clock in the widget. From that app you can set alarms, timers, and more. After upgrading to GB, this no longer works though I think it may have to do with running the Clock app from the App list first.
After updating to GB yesterday, I believe that I was able to use the Alarm/Clock function from the widget at least once. Since that time, I ran the Clock app from the All Apps screen and now the Widget no longer calls up the Clock App and the Clock app itself has disappeared from the App list.
I think the root of the problem is the missing Clock app. Do NOT want to factory reset to get this back. There must be another way.
For those having this problem, is your Clock app missing?
Is there a way to reinstall just the Clock app?